Cancer is a class of diseases in which a group of cells display uncontrolled growth (division beyond the normal limits), invasion (intrusion on and destruction of adjacent tissues), and sometimes metastasis (spread to other locations in the body via lymph or blood). These three malignant properties of cancers differentiate them from benign tumors, which are self-limited, and do not invade or metastasize. Most cancers form a tumor but some, like leukemia, do not.
Cancer may affect people at all ages, even fetuses, but the risk for most varieties increases with age. Cancer causes about 13% of all human deaths. According to the American Cancer Society, 7.6 million people died from cancer in the world during 2007. Cancers can affect all animals.
Nearly all cancers are caused by abnormalities in the genetic material of the transformed cells. These abnormalities may be due to the effects of carcinogens, such as tobacco smoke, radiation, chemicals, or infectious agents. Other cancer-promoting genetic abnormalities may be randomly acquired through errors in DNA replication, or are inherited, and thus present in all cells from birth. The heritability of cancers are usually affected by complex interactions between carcinogens and the host's genome. New aspects of the genetics of cancer pathogenesis, such as DNA methylation, and microRNAs are increasingly recognized as important.
Most cancers are initially recognized either because signs or symptoms appear or through screening. Neither of these lead to a definitive diagnosis, which usually requires the opinion of a pathologist, a type of physician (medical doctor) who specializes in the diagnosis of cancer and other diseases.
People with suspected cancer are investigated with medical tests. These commonly include blood tests, X-rays, CT scans and endoscopy. A cancer may be suspected for a variety of reasons, but the definitive diagnosis of most malignancies must be confirmed by histological examination of the cancerous cells by a pathologist. Tissue can be obtained from a biopsy or surgery. Many biopsies (such as those of the skin, breast or liver) can be done in a doctor's office. Biopsies of other organs are performed under anesthesia and require surgery in an operating room.
The existing diagnostic tests for cancer are thus often unpleasant for the patient and may be risky for the health (X-ray, surgery . . . ). There is therefore a need for a non invasive and reliable diagnostic test of cancer, that can be performed routinely and in the usual practice or laboratories.
The present invention disclosed a reliable and sensitive diagnostic method applied to the saliva of human subjects.
Saliva is a clear, slightly acidic fluid that contains a number of inorganic and organic constituents important to oral health. Whole saliva is a mix of secretions from major and minor salivary glands and gingival crevicular fluid, which contains sloughed host cells, bacteria and food debris. Therefore, saliva is not a passive “ultrafiltrate” of serum, but contains a distinctive composition of enzymes, hormones, antibodies, and other molecules (Rehak, N. N. et al. 2000 Clin Chem Lab Med 38:335-343; Wong D T, American Scientist, vol 96, 2008). For example, saliva contains a large number of proteins that aid in the protection of oral cavity tissues, including mucins, amylases, agglutinins, lisozymes, peroxidases, lactoferrin and secretory IgA. Whole saliva contains normal epithelial cells and leukocytes that can be pelleted, and from which one can easily recover genomic DNA and mRNA, potentially used to find genomic markers of several diseases. Indeed, most of the DNA or RNA extracted from crude saliva was found to be of viral or bacterial origin (Stamey, F. R. et al. 2003 J Virol Methods 108:189-193; Mercer, D. K. et al. 2001 FEMS Microbiol Lett 200:163-167) and of human extra or intracellular origin. Also, many groups have focused their study and diagnostic tests on the supernatant and thus cell-free phase of whole saliva, which contains many analytes such as free mRNA (Zimmermann B G et al, Oral Oncology 2008, 44, 425-429).
In the past 10 years, the use of saliva as been successfully applied in diagnostics (Streckfus, C F. & Bigler, L. R. 2002 Oral Dis 8:69-76). Diagnostic biomarkers in saliva have been identified for monitoring caries, periodontitis, salivary gland diseases, and systemic disorders, e.g., hepatitis and HIV (Lawrence H. P. et al, 2002 J Can Dent Assoc 68: 170-174). Also, oral bacteria have been reported to be elevated in oral and esophageal cancer lesions (Mager D. L. et al. J Transl Med. 2005; 3: 27, Hooper J. S et al., Journal of Clinical Microbiology, May 2006, P 1719-1725). The reason for these shifts in bacterial colonization of cancer lesions is unclear. Mechanistic studies of bacterial attachment provide some insights and research has repeatedly shown that oral bacteria demonstrate specific tropisms toward different biological surfaces in the oral cavity such as the teeth, mucosa, and other bacteria. There is less time in oral cavity, for a complex biofilm to develop on soft tissue surfaces; thus, a premium is placed on potent mechanisms of adhesion. The differences in bacterial tropisms for specific oral sites suggest that different intra-oral surfaces and bacterial species have different receptors and adhesion molecules that dictate the colonization of different oral surfaces. Certain glycoconjugates serve as receptors for specific bacteria and recent reports support the notion that shifts in the colonization of different cancer cells are associated with observed changes in cell surface receptors. Hence, Mager D. L. et al showed that the salivary microbiota in subjects with an oral squamous cell carcinoma (OSCC) lesion differs from that found in OSCC-free controls. Bacterial counts were determined for each species, averaged across subjects in the 2 subject groups, and significance of differences between groups determined using the Mann-Whitney test and adjusted for multiple comparisons; interestingly, it appeared that the bacteria strains Capnocytophaga gingivalis, Prevotella melaninogenica, Streptococcus mitis and Micrococcus luteus were particularly present in patients having OSCC and were therefore suggested to serve as diagnostic markers for oral cancer. However, as it is demonstrated in (ref), these particulate bacteria strains were poorly associated with oral cancer (a maximal sensitivity of 80%) (Mager D. L. et al). Also, it has been shown in Li et al (Journal of Applied Microbiology, 2004, 97, 1311-1318) that the presence in saliva of significant high numbers of specific alive bacteria (40 different strains have been identified in this study and more than 200 specific alive bacteria have been described in the oral cavity), could be associated to the biofilm formation, colonization of the oral cavity and lack of oral hygiene that are often associated to oral cancer development in developing countries. However, one can not predict from Li et al that the particulate strains Capnocytophaga gingivalis, Prevotella melaninogenica, Streptococcus mitis and Micrococcus luteus can serve as reliable diagnostic markers for human oral cancer.
Interestingly, the use of the saliva has never been proposed for a diagnostic test intended to detect human cancer.
Saliva is a mixture of secretions from multiple salivary glands, including the parotid, submandibular, sublingual and other minor glands lying beneath the oral mucosa. As mentioned before, human saliva harbors a wide spectrum of peptides and proteins that constitutes the human salivary proteome. What has been less studied is the presence of organic biochemical compounds in the saliva.
Biochemical organic compounds can be enzymes, hormones, inorganic ions, peptides, proteins, carbohydrates, vitamins, lipids, fatty acids and volatile compounds. They can be measured by many techniques and devices, either optical technologies (for example laser absorption spectroscopy, mid infra red absorption spectroscopy, laser magnetic resonance spectroscopy, proton transfer reaction mass spectrometry . . . ) or non-optical technologies (gas chromatography, mass spectrometry, etc. . . . ) (Mashir A, Advanced Powder Technology, 2009).
Only one study has ever compared the biochemical organic content of a fraction of saliva from healthy or sick-patients (Volozhin et al. Stomatologiia (mosk), 2001; 80(1):9-12). In this study, patients with chronic generalized periodontitis and patients with chronic generalized gingivitis and periodontitis have been tested with air from the oral cavity and liquid samples were collected by washing the oral cavity with sterile water. Chemical compounds of the air and the washed liquid were analyzed by chromato-mass-spectrometry, gas-adsorption and gas-liquid chromatography. The content of dimethyl sulphide, dimethyl disulphide increased in the oral air and such volatile short chain fatty acids (VSCFA) as butyrate, propionate, acetate rose, but their aldehydes (butyraldehyde, acrolein, acetaldehyde) decreased in oral fluid during periodontitis. It was also shown that volatile short-chain fatty acids (propionate, butyrate and acetate) of bacterial and tissue origin are important factors of pathogenesis of oral tissue inflammation (Volozhin et al. Stomatologiia (mosk), 2001; 80(1):9-12). In this study, the organic compounds have been analyzed in air from the oral cavity and rincing liquid collected by washing the oral cavity with sterile water but not in the volatile fraction of the raw saliva.
Contrary to saliva, the presence of volatile organic molecules in exhaled breath has been well studied and was shown to contain a lot of biochemical organic compounds: in 1971, using gas-liquid partition chromatography analysis, Linus Pauling demonstrated the presence of 250 substances in exhaled breath (Pauling L. et al. Proc. Natl. Acad. Sci. USA 68 (1971) 2374-2376). In 1990, the development of very sensitive modern mass spectrometry (MS) and gas chromatography mass spectrometry (GC-MS) instruments, gives identity to thousands of unique substances in human exhaled breath (Mashir A, Advanced Powder Technology, 2009). These substances include elemental gases like nitric oxide and carbon monoxide and a multitude of other volatile organic compounds. Furthermore, exhaled breath also carries aerosolized droplets collected as exhaled breath condensate that have non-volatile compounds that can be captured by a variety of methods and analyzed for a wide range of biomarkers from metabolic end products to proteins. Breath analysis is now used to diagnose and monitor asthma, pulmonary hypertension, respiratory diseases, gastrointestinal diseases, critical illness, to check for transplant organ rejection, and to detect lung cancer, and breast cancer (Mashir A, Advanced Powder Technology, 2009; Chan H. P. et al, Lung Cancer, 2009). However, it is noteworthy that breath analysis has never been proposed to detect oral cancer in human subject.
Interestingly, it appeared that the biochemical organic molecular composition of saliva has never been compared between patients suffering from cancer and healthy individuals. Moreover, the biochemical organic molecular composition of the volatile fraction of saliva has never been studied so far to detect epithelial cancer, non-epithelial cancer, as well as those of solid and non-solid cancers. Cancers consisting of epithelial cancer cells include, for example, lung cancer, breast cancer, gastric cancer, colorectal cancer, uterine cervical cancer, uterine cancer, oral cancers, i.e. cancer of the oral cavity (e.g., laryngeal cancer, pharyngeal cancer, lingual cancer, etc.), cancer of the oropharynx, oropharyngeal squamous cell carcinoma (OSCC), or head and neck squamous cell carcinoma, prostate cancer, colon cancer, squamous cell carcinoma, including, adenocarcinoma and the like; cancers consisting of aforementioned non-epithelial cancer cells (sarcoma) include, for example, liposarcoma, osteosarcoma, chondrosarcoma, rhabdomyosarcoma, leiomyosarcoma, fibrosarcoma, angiosarcoma, and the like.
The volatile fraction corresponds to the evaporated part of the fluid fraction of saliva. This volatile fraction contains some organic compounds that are not found in the raw saliva sample without the evaporation process, even after its filtration.
Also, it is important to note that the molecular content of saliva is not comparable at all to the composition of exhaled breath, which is mostly a reflect of lung molecules (Song G, et al. Quantitative breath analysis of volatile organic compounds of lung cancer patients, Lung Cancer (2009)). Hence, the molecular composition of the volatile fraction of saliva can not be inferred from the data issued from the breath analysis. To date, no exhaustive analysis of the biochemical content of the volatile fraction of saliva has never been disclosed, a fortiori in the context of cancer.
One of the values of saliva is the ease of sampling and subject compliance for sample collection, which includes field applications as well as home collection. However, the study of the biochemical compounds present in saliva (either in fluid or in the volatile fraction) for clinical application appeared to be difficult since it is necessary to stabilize and maintain their integrity for at least several days at room temperature.
It has already been shown that the RNAprotect® Saliva reagent (RPS, Qiagen Inc, Valencia, Calif.) could stabilize RNA in samples at room temperature for up to 12 weeks (Park N J, Clin Chem 2006; 52:2303-4). Also, Jiang J et al showed that it is possible to use the RPS for stabilization of DNA and proteins in saliva only when endogenous cells are previously removed by centrifugation or by filtration (Jiang J et al, Archives of Oral Biology, 2008).
However, as far as biochemical organic compounds are concerned, they are degraded by the microflora, food and dental care products at room temperature. Importantly, nobody has ever proposed a way to protect these sensitive compounds from the degradation occurring at room temperature.
Therefore, it is still a major challenge to stabilize all the components of saliva, especially organic compounds, without any filtration or centrifugation steps, for a long time at room temperature.
In this context, the present inventors show here for the first time that:                i) it is possible to stabilize organic compounds present in saliva during at least 10 days in an appropriate buffer,        ii) it is possible to extract a volatile fraction from a sample of stabilized saliva, and to detect therein several organic volatile compounds in a significant amount,        iii) it is possible to detect a high risk of developing cancer by analyzing the level of only few particular biochemical compounds in said volatile fraction of stabilized saliva.        
Importantly, it is to note that no test for predicting and/or diagnosing cancer using the volatile fraction of saliva has ever been proposed so far.
More importantly, the particular biochemical compounds hereafter identified have never been associated with cancer so far.
The present invention therefore discloses:                i) a method for stabilizing crude saliva samples of human subjects,        ii) a method for extracting the volatile fraction of stabilized saliva samples, and to analyze its content in biochemical organic compounds,        iii) a method for detecting a high risk of developing cancer, by analyzing the level of particular organic biochemical compounds in the volatile fraction of stabilized saliva.        
Finally, specific combinations of biological parameters associated with high risk of cancer have been identified, highlighting that it is possible to obtain a reliable and sensitive prognosis/diagnosis test of cancer from a unique sample of stabilized saliva.